Stronger integration with Chimera provides an opportunity not just for viaualization of gerenated trajectories and structures, but for a better control of the workflow for Adun simulations. Aspects of this integration include:
1) visualization of Adun trajectories
2) preparations of PDBs prior to the building of the corresponding systems in Adun (side chain completion, hydrogens addition, parameters graphical editing...)
3) steered MD, by controling (almost) at run time trajectories and producing changes in the topology and FF that automatically transfer to Adun to rebuild the system and restart the simulations
4) simple minimizations and relaxations from a chimera extension (check, eg, existing plugins for Dock or AMBER in chimera)
5) others

To start with, the task will include exploring and eventually cloning the way Chimera and Cytoscape are connected through the Cytoscape StructureViz plugin. This is a bidirectional plugin that uses command line tools to access chimera from cytoscape and viceversa.

A second option would be exploring the use of web services, although this can be left for the second generation of the Adun/chimera integration and may be replaced by the builtin distributed computing with Adun (check how Blast is run from chimera)

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